ABSTRACT
Invasive species are among the most important, growing threats to food security and agricultural systems. The Mediterranean fruit fly Ceratitis capitata  is one of the most damaging representatives of a group of rapidly expanding species in the family Tephritidae due to their wide host range and high invasiveness. Here, we used restriction site-associated DNA sequencing (RADseq) to investigate population genomic structure and phylogeographic history of medflies collected from six sampling sites, including Africa (South Africa), the Mediterranean (Spain, Greece), Latin America (Guatemala, Brazil) and Australia. A total of 1,907 single nucleotide polymorphisms (SNPs) showed two genetic clusters separating native and introduced ranges, consistent with previous findings. In the introduced range, all individuals were assigned to one genetic cluster except for those in Brazil, which showed introgression of a genetic cluster that also appeared exclusively in South Africa and could not be previously identified using microsatellite markers. Moreover, the microbiome variations in medfly populations from selected sampling sites was assessed by amplicon sequencing of the 16S ribosomal RNA (V4 region). No strong patterns of microbiome variation were detected across geographic regions or host plants, except for the differentiation of the Brazilian specimens which showed increased diversity and unique composition of its microbiome compared to other sampling sites. The unique SNP patterns in the Brazilian specimens could point to a direct migration route from Africa with subsequent adaptation of the microbiota to the specific conditions present in Brazil. These findings significantly improve our understanding of the evolutionary history of global medfly invasions and adaptation to newly colonised environments.
INTRODUCTION
Drastic environmental changes affecting natural and anthropogenic ecosystems involve massive shifts in species’ geographical distributions and cause worldwide invasions facilitated by the ability of certain species to adapt to newly colonised environments (Heino, Virkkala, & Toivonen, 2009). Invasive species have been associated with an estimated 1.3 trillion USD in economic losses and are responsible for diminishing local species richness (Diagne et al., 2021). Therefore, frequent interventions are required to control the damaging effects of invasive species from new colonisation events. Large-scale range expansions and intervention measures for pest control (e.g., pesticides, Sterile Insect Technique (SIT)) have profound but poorly characterised effects on population structure, invasion pathways, and adaptation to local environments. Among agricultural insect pests, the family Tephritidae (fruit flies) harbours several rapidly expanding species of great concern, including the Mediterranean fruit fly Ceratitis capitata  (Wiedemann, 1824) (commonly known as medfly), a cosmopolitan, polyphagous species with over 250 different hosts of fruit and vegetables (White & Elson-Harris, 1992). In the past two centuries, C. capitata  has expanded from a presumed origin in Sub-Saharan Africa to the Mediterranean basin and later spread to tropical regions in all continents (Gasperi, Guglielmino, & Milani, 1991; Malacrida et al., 2007; Malacrida et al., 1992). Its range can shift with climate change and commercial trade (Gutierrez & Ponti, 2011; Hill et al., 2016). It is considered one of the most successful invaders worldwide and a significant economic pest to the fruit market, estimated to cost more than 2 billion USD annually in losses (Sciarretta et al., 2018).
Differences in local climate and exposure to various host plants and natural enemies, reinforced by large geographic distances, may have constrained gene flow, and resulted in differentiation of medfly populations. Current knowledge of medfly population genetics supports low levels of intercontinental connectivity between the native and colonised ranges (Elfékih, Makni, & Haymer, 2010; Gasperi et al., 2002; Karsten, Jansen van Vuuren, Addison, Terblanche, & Leung, 2015) but the rate of dispersal among introduced populations remains unclear, especially in Central and South America (Arias, Elfekih, & Vogler, 2018; Deschepper et al., 2021; Ruiz-Arce et al., 2020), despite its importance for implementing pest control strategies. One of the potential factors influencing the medfly’s propensity for dispersal and adaptation to new environments is the interaction between the microbiome and its host. It has been previously reported that specific microbiome variants exist synergistically with insect hosts and might rapidly spread across populations (Aharon et al., 2013). Evidence from Drosophila melanogaster  Meigen, 1830 suggests that shifts in microbiome composition can alter population dynamics and, consequently, might be considered a relevant driver of ecological and evolutionary processes at the population level (Rudman et al., 2019). The medfly receives its microbiota during oviposition via maternal inheritance (Behar, Jurkevitch, & Yuval, 2008). The composition during larval development is restructured, with microbial community shifts occurring at different stages (Aharon et al., 2013; Malacrino, Campolo, Medina, & Palmeri, 2018). Such knowledge dramatically enhances our understanding of the influence of the microbial profile on insect development. Exploring potential shifts of microbiota in introduced ranges could reveal further information regarding the medfly’s colonisation patterns.
The emergence of next-generation sequencing, including reduced representation genome sequencing techniques such as Restriction Associated DNA-tags sequencing (RADseq), has made it possible to study the population diversity of non-model organisms at the genomic level (Andrews et al., 2016, Davey & Blaxter, 2010). For example, RADseq has been used to address biological questions on demography and dispersal of invasive insect pests (Elfékih et al. 2018; McCormack, Hird, Zellmer, Carstens, & Brumfield, 2013; Schmidt et al. 2020), patterns of gene flow, phylogeography, and species delimitation (Eaton et al., 2013; Elfékih et al. 2021; Emerson et al., 2010; Dong et al. 2021), microbial association and local adaptation (Orantes et al. 2018; van Oppen et al. 2018).
Using RADseq data, we present the genetic relationships, gene flow patterns, possible pathways of invasions, and cross-continent colonisation routes of medfly populations collected from six regions distributed worldwide. In addition, we examine genome-wide SNP variation and explore the bacterial microbiome profile associated with each sampling site and its possible correlation with the medfly presumed dispersal routes.